From RPONEC@icpf.cas.cz Tue Sep 3 02:52:50 1996 Received: from beba.cesnet.cz for RPONEC@icpf.cas.cz by www.ccl.net (8.7.5/950822.1) id CAA16060; Tue, 3 Sep 1996 02:18:26 -0400 (EDT) Received: from msgw.icpf.cas.cz (MSGW.ICPF.CAS.CZ [193.84.116.5]) by beba.cesnet.cz with SMTP id IAA26530 (8.6.12/IDA-1.6 for ); Tue, 3 Sep 1996 08:18:17 +0200 Received: by msgw.icpf.cas.cz with Microsoft Mail id <322C4C74@msgw.icpf.cas.cz>; Tue, 03 Sep 96 08:19:16 PDT From: "Ponec, Robert" To: "'CCL'" Subject: PSI88 Date: Tue, 03 Sep 96 08:21:00 PDT Message-ID: <322C4C74@msgw.icpf.cas.cz> Encoding: 17 TEXT X-Mailer: Microsoft Mail V3.0 Dear all, sometime ago I have downloaded from a FTP server the program package PSI88 for drawing wave functions. I was able to compile and to run most of the programs included in the package but because some of these programs use the CALCOMP graphic routines my fortran compiler (Fortran Power station v. 4.0) is unable to compile them. My question is whether the CALCOMP graphic routines or at least manuals for them can be obtained somewhere or whether there is some other program package for drawing wave functions or densities which does not require CALCOMP. Many thanks, dr. Robert Ponec Institute of Chemical Process Fundamentals, Czech Academy of Sciences Prague 6, Suchdol Czech Republic e-mail: rponec@icpf.cas.cz From BIOCHROS@mol.uj.edu.pl Tue Sep 3 07:52:50 1996 Received: from if.uj.edu.pl for BIOCHROS@mol.uj.edu.pl by www.ccl.net (8.7.5/950822.1) id HAA17077; Tue, 3 Sep 1996 07:51:50 -0400 (EDT) Received: from mol.mol.uj.edu.pl (mol.mol.uj.edu.pl [149.156.76.2]) by if.uj.edu.pl (8.7.1/8.7.1) with SMTP id NAA20494 for ; Tue, 3 Sep 1996 13:56:34 +0200 (MET DST) Received: from MOL/MAILQUEUE by mol.mol.uj.edu.pl (Mercury 1.11); Tue, 3 Sep 96 12:49:03 GMT+2 Received: from MAILQUEUE by MOL (Mercury 1.11); Tue, 3 Sep 96 12:48:35 GMT+2 From: "Zaklad Fizjologii i Biochemii Roslin" To: chemistry@www.ccl.net Date: Tue, 3 Sep 1996 12:48:29 GMT+2 Subject: abinitio&quinones Priority: normal X-mailer: PMail v3.0 (R1a) Message-ID: Dear Netters, I would like to ask you a question about abinitio simulations of quinones. Would anyone give me any references connected with abinitio or semiempirical simulations of plastoquinones, ubiquinones or other quinones. I am interested in partial charges of these compounds and molecular dynamics of biological membranes containing quinones or other compounds related to them, using Amber. I should be very grateful for any help. Thank you in advance. Malgorzata Jemiola-Rzeminska MJR@mol.uj.edu.pl From Knut.Asmis@unifr.ch Tue Sep 3 08:52:54 1996 Received: from swifr9 for Knut.Asmis@unifr.ch by www.ccl.net (8.7.5/950822.1) id HAA17083; Tue, 3 Sep 1996 07:52:05 -0400 (EDT) Received: from sgpch1.unifr.ch by swifr9 with SMTP (PP); Tue, 3 Sep 1996 13:49:55 +0200 Received: from pchpc01.unifr.ch by sgpch1.unifr.ch via SMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI) for id NAA00673; Tue, 3 Sep 1996 13:50:41 +0200 Date: Tue, 3 Sep 1996 13:50:41 +0200 Message-Id: <199609031150.NAA00673@sgpch1.unifr.ch> X-Sender: asmis@sgpch1.unifr.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Knut.Asmis@unifr.ch (Knut Asmis) Subject: Three Electron Problem / ZINDO output X-Mailer: Dear netters, I encounter a problem when performing CI calculations on doublet states with the ZINDO program. The problem is related to the so called "Three electron problem", which deals with the question: "What are the wavefunctions describing the true spin states, e.g. eigenfunctions of the total spin operator S^2 and of the z-component spin operator Sz, for a system of three electrons and three spaceorbitals". My question doesn't concern the "three electron problem" itself, but the way computational programs like ZINDO refer to Slater determinants or in this case linear combinations of Slater determinants. The ZINDO output generally relates the CI coefficients to the appropriate Slater determinants (e.g. "antisymmetrized" electron configurations) by a numbering scheme. For example the following scheme (1) 1 2 3 4 5 1 2 3 4 identifies the electron configuration, in which the spaceorbitals 1 to 4 are doubly occupied and the orbital 5 is occupied by a single electron with spin alpha. What about the following case ? (2) 1 2 3 4 6 1 2 3 5 The Slater determinant, corresponding to an electron configuration with three unpaired electrons in the spaceorbitals 4, 5 and 6 is not an eigenfunction of the total spin operator S^2. Only the appropriate linear combination of Slater determinants is an eigenfunctions of S^2. My question is: What linear combination of Slater determinants is associated with the general numbering scheme (3)? (3) a c b My answer would be: (3): 1/sqrt(2) * ( DET(aBc) - DET(Abc) ) In this case DET(aBc) refers to the Slater determinant, which is related to the electron configuration in which electron 1 occupies orbital a and has spin alpha, electron 2 occupies orbital b and has spin beta (indicated by the capital letter), and electron 3 occupies spaceorbital c and has spin alpha. DET(Abc) refers to the Slater determinant, which is related to the electron configuration in which electron 1 occupies orbital a and has spin beta, electron 2 occupies orbital b and has spin alpha and electron 3 occupies spaceorbital c and has spin alpha. Is this correct? Thank you in advance for suggestions or answers, Knut Asmis Institut for Physical Chemistry University of Fribourg Switzerland e-mail: knut.asmis@unifr.ch From SHIL@dtpax2.ncifcrf.gov Tue Sep 3 11:52:54 1996 Received: from dtpax2.ncifcrf.gov for SHIL@dtpax2.ncifcrf.gov by www.ccl.net (8.7.5/950822.1) id LAA17878; Tue, 3 Sep 1996 11:02:31 -0400 (EDT) From: Date: Tue, 3 Sep 1996 11:03:43 -0400 (EDT) To: chemistry@www.ccl.net Message-Id: <960903110343.202148e9@dtpax2.ncifcrf.gov> Subject: Comp Chem & Drug Design Journals Dear CCLers: Has anyone of you compiled or seen a list of Journals which are mainly devoted to Computational Chemistry and/or Drug Design? Are the any web sites where I can find this? Related information such as citation rate would be helpful. Thanks. Leming Shi shil@dtpax2.ncifcrf.gov From mlebret@igr.fr Tue Sep 3 12:43:56 1996 Received: from fw for mlebret@igr.fr by www.ccl.net (8.7.5/950822.1) id LAA18077; Tue, 3 Sep 1996 11:47:36 -0400 (EDT) Received: by fw; (5.65v3.2/1.3/10May95) id AA18283; Tue, 3 Sep 1996 17:53:36 +0200 Received: from myc (myc.igr.fr) by igr.fr (PMDF V5.0-3 #14715) id <0DX5YMU7D000B1@igr.fr> for chemistry@www.ccl.net; Tue, 03 Sep 1996 17:49 +0200 (MET) Received: by myc (940816.SGI.8.6.9/930416.SGI.AUTO) for chemistry@www.ccl.net id SAA20715; Tue, 03 Sep 1996 18:51:52 +0200 Date: Tue, 03 Sep 1996 18:51:52 +0200 From: mlebret@igr.fr (Marc Le Bret) Subject: Error in Force output in G94 To: chemistry@www.ccl.net Message-Id: <199609031651.SAA20715@myc.igr.fr> Content-Transfer-Encoding: 7BIT Dear G94 users I have a problem in the log file After a geometry optimisation under constraint, the force under the line Center Atomic Forces (Hartrees/Bohr) seems to be right, but differs from the value -DE/DX written under Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total) Is there any reason for that ? ****************************************************************** * Marc Le Bret * * Laboratoire de Physicochimie et de Pharmacologie * * des macromolecules biologiques CNRS URA147 * * Institut Gustave Roussy 94805 Villejuif Cedex France * * mlebret@igr.fr Tel (33 1) 45 59 49 79 FAX (33 1) 46 78 41 20 * ****************************************************************** From jeremy@med.su.oz.au Tue Sep 3 12:52:53 1996 Received: from blackburn.med.su.oz.au for jeremy@med.su.oz.au by www.ccl.net (8.7.5/950822.1) id MAA18252; Tue, 3 Sep 1996 12:14:23 -0400 (EDT) Received: (jeremy@localhost) by blackburn.med.su.oz.au (8.6.11/8.6.4) id CAA16467 Wed, 4 Sep 1996 02:14:22 +1000 From: Jeremy R Greenwood Message-Id: <199609031614.CAA16467@blackburn.med.su.oz.au> Subject: SCRF and pKa To: chemistry@www.ccl.net Date: Wed, 4 Sep 1996 02:14:21 +1000 (EST) Cc: jeremy@blackburn.med.su.oz.au (Jeremy R Greenwood) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Greetings all, Two related and maybe naive questions on the difficult problem of aqueous phase calculations: I'm studying some acidic tautomeric heterocycles; while molecular dynamics methods or semi-empirical (e.g. SAM1) may be recommended, I'm interested in ab initio continuum methods, not least because I have them readily available. 1) Can someone point me in the direction of a study of, or give me an opinion of, the reliablity of the IPCM model vs. other (SCRF) methods for calculating solvation energies of species in dilute aqueous solution. I'm particularly interested in species for which hydrogen bonding is likely to be significant, and the comparative treatment of hydroxy vs. oxo tautomers. My preliminary IPCM results consistantly indicate greater aqueous stabilisation of hydroxy vs. oxo tautomers, apparently in contradiction both with published results >from other methods (FEP, Onsage, PCM) and generally accepted wisdom if I understand correctly. 2) I'm interested in the state of the art for the ab initio calculation of pKa. I'd greatly appreciate comments & suggestions for methodology, or pointers to recent literature. Empirical attempts within a given system to correlate dipole moments or point charges on acidic moieties calculated from one or other method with pKa could be a possible avenue. Is this tried? A means of attacking pKa with SCRF I'm considering: in order to make most use of cancellation of systematic error, modelling the overall reaction: HA + OH- -> A- + H2O Good estimates of the gas-phase deltaG of reaction should be calculable, using Hartree-Fock frequencies and correllated theories with diffuse functions for energies. An accurate estimate of deltaG in dilute aqueous solution at 298K should lead to pKa. How best to go from the former to the latter? IF (from question 1) the IPCM model (or other SCRF) gives reasonable relative aqueous solvation single point energies from gas phase geometries, could these be simply be used to correct the gas-phase free energies to determine an aqueous phase free energy of reaction and hence pKa with any degree of confidence? Alternatively, as opposed to single point calculations, optimisation and frequency calculations could be performed with SCRF for aqueous solution, and from these, the free energy of reaction in solution derived and hence pKa. However, Gaussian94 only offers these calculations for the Onsager model using uncorrelated theories, and I have my doubts as to how well this would handle such systems. Thanks for any suggestions in advance, Jeremy From iiv@mmlds1.pha.unc.edu Tue Sep 3 13:52:54 1996 Received: from mmlds1.pha.unc.edu for iiv@mmlds1.pha.unc.edu by www.ccl.net (8.7.5/950822.1) id NAA18622; Tue, 3 Sep 1996 13:49:21 -0400 (EDT) Received: by mmlds1.pha.unc.edu (5.57/TAS/11-16-88) id AA15179; Tue, 3 Sep 96 13:59:20 -0400 Date: Tue, 3 Sep 1996 13:59:19 -0400 (EDT) From: Iosif Vaisman To: CHEMISTRY@www.ccl.net Subject: Computational Molecular Biology Workshop, October 15-19, 1996 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CAROLINA WORKSHOPS University of North Carolina at Chapel Hill Computational Molecular Biology October 15 - 19, 1996 This course is designed for scientists with limited prior experience in computational molecular biology. The topics to be covered include: biomolecular informatics and databases, protein and nucleic acid sequence analysis and alignment, 3D protein structure analysis and prediction, molecular modeling and dynamic simulations of proteins and nucleic acids, and structure-based drug design. The workshop will consist of the in-depth theoretical lectures and intensive hands-on laboratory sessions. CAROLINA WORKSHOPS are intensive hands-on courses designed to teach cutting edge methods in molecular biology and biotechnology. Four or five courses on different topics in molecular biology and/or biotechnology are offered each year. The courses are designed for novice students as well as for individuals with prior experience. All students benefit from in-depth interaction with instructors. To apply, send a curriculum vitae and a brief letter describing your research interests and their relevance to the Workshop. Applicants should contact the program office as soon as possible. Please indicate your complete mailing address and telephone/fax number. Application Deadline-September 7, 1996. Tuition - $ 1,200.00. Participation is limited to 15 people. COURSE DIRECTOR: Alexander Tropsha, Ph.D., University of North Carolina at Chapel Hill INSTRUCTORS: Frank K. Brown (Glaxo-Wellcome) Alexander Tropsha (UNC-Chapel Hill) Wayne Litaker (UNC-Chapel Hill) Iosif I. Vaisman (UNC-Chapel Hill) David C. Richardson (Duke University) For further information or to apply, contact: Dr. Wayne Litaker, Facility Director University of North Carolina at Chapel Hill Program in Molecular Biology & Biotechnology 442 Taylor Hall CB 7100 Chapel Hill, North Carolina 27599-7100 TELEPHONE (919) 966-1730, FAX (919) 966-6821 E-MAIL litaker@med.unc.edu From dan@sage.syntex.com Tue Sep 3 14:53:20 1996 Received: from sage.syntex.com for dan@sage.syntex.com by www.ccl.net (8.7.5/950822.1) id NAA18648; Tue, 3 Sep 1996 13:53:43 -0400 (EDT) Received: (from dan@localhost) by sage.syntex.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA10225 for CHEMISTRY@www.ccl.net; Tue, 3 Sep 1996 10:53:38 -0700 From: dan@sage.syntex.com (Dr. Daniel L. Severance) Message-Id: <9609031053.ZM10224@sage.syntex.com> Date: Tue, 3 Sep 1996 10:53:38 -0700 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Re:Psi88 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii > Dear dr.Severance, > few days ago I have downloaded from the ftp the program package PSI88, > version 1.0 for the graphical display of wavefunctions. I have been able > to compile and to run most of the programs but because my compliler does > not have (it is the fortran power station 4.0) the CALCOMP routines I was > not able to compile the program psi2 which allows the display of > wavefunctions on the screen. I think that it would be possible to replace > the calls for calcomp routines by the call of analogous graphic routines > for my compiler but this would require to know what exactly the graphic > calcomp routines do. This is why I would like to ask you whether it is psplot.f contains calcomp -> postscript routines. If you want postscript output just compile psi2.f and psplot.f together. Look at the Makefile definition for compiling PSI2PS (postscript). Also, you'll find definitions for compiling HPGL, ChemText Metalfile (I don't know if that's the same as ISIS uses these days), and GKS (not tested in a long time). > I have yet another question. In the source programs there is at several > places written that the program in addition to drawing wave functions > (orbitals) the program should be able to draw also the 3-D and 2-D > density contours but I am not sure whether in the version 1.0 which I > have these options are indeed enabled. This is why I would also like to > ask you whether such drawings are possible with the program I have or > whether there is some newer release of the program which can do it. I generally use the G94 cubedensity function to write out a density cube directly. The PSICON program can be pretty easily modified to read a density cube of that format. (PSI1 writes out a cube of orbital values). The programs PSI1 and PSICON were split (they were 1 program in PSI77) for just that purpose. You can generate your cube anywhere, and then read them into PSICON followed by PSI2PS. Good luck! Dan -- Dr. Daniel L. Severance dan@sage.syntex.com Nebraska Staff Researcher Work phone:(415) 354-7509 College Football Roche Bioscience (Syntex) Fax (Work):(415) 852-1875 National Champions R6W-002, 3401 Hillview Ave Palo Alto, CA 94303 1994,1995